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Allan was born on November 12, 1837, at Winchester Gardens, near Winchester, one of two children,
both sons, of Thomas Allan and Jane Dowdell George Allan. After being educated in a
local private school, he taught in Jefferson County and in Winchester to earn enough money to enroll in the
University of Virginia in 1857. Allan excelled at debate and graduated with honors in
1860 with an MA in applied arithmetic. He moved to Loudoun County where he was assistant to the
principal of Bloomfield Academy when the Civil War began.

Allan enlisted in the Confederate army and served as a clerk in the quartermaster
department under Stonewall Jackson. In 1862, sponsored by University of Virginia
classmate Alexander "Sandie"
Pendleton, Allan took the ordnance officer examination. He passed with the
highest score and on December 27, 1862, became a captain of artillery. On January 19, 1863, he
was appointed to Jackson's staff as chief of ordnance of the Second Corps, Army of
Northern Virginia. He served throughout the war, advancing to the rank of major on
April 25, 1863, and lieutenant colonel on March 28, 1864. He was assigned to Jubal
Early's Shenandoah Valley
command on March 1, 1865.

After the war Allan took a job as cashier of the National Valley Bank in Staunton. In 1866 he accepted an
invitation from Robert E. Lee, then president of Washington College in Lexington, to
join the faculty as professor of applied mathematics. For almost eight years he
taught there and published three books on applied mechanics between 1873 and 1875,
all of which were reprinted shortly after his death.

While at Washington College, Allan wrote the first of many articles and books on the
Civil War. He collaborated with Jedediah Hotchkiss on The
Battle-fields of Virginia: Chancellorsville (1867) and also wrote a long
unsigned article on the Battle of Gettysburg that appeared in the Southern Review in 1869. The piece on Gettysburg benefited from his
interviews with Lee and was the first of a great many articles Allan wrote, so many
that altogether they probably contained more words than his books. He became a
popular figure on the lecture circuit and at commemorative ceremonies, and he
published articles and speeches in Century, the Nation, and the Magazine of American
History, but most of his articles, reviews, and commemorative pieces appeared
in the Southern Historical Society Papers. His 1866 memoir of
his own field ordnance service has been pronounced "priceless."

Allan's published work on the causes, conduct, and significance of the Civil War not
only placed a substantial body of reliable information on the record, but also helped
establish the literary genre of the Lost Cause. Allan's most enduring and useful
volumes on the Civil War were the History of the Campaign of Gen.
T. J. (Stonewall) Jackson in the Shenandoah Valley of Virginia (1880), which
was reprinted several times with variant titles and reissued in 1974, and The Army of Northern Virginia in 1862 (1892), published
posthumously, the first part of an intended complete wartime history of Lee's
army.

On November 21, 1873, Allan was elected the first principal of McDonogh Institute, an
endowed private school for poor boys at Owings Mills, near Baltimore, Maryland. He
married Elizabeth Randolph Preston, daughter of a professor at the Virginia Military Institute, John Thomas
Lewis Preston, on May 14, 1874, and they had two daughters and three sons. She was
active for many years in the Presbyterian Church, in promoting Sunday schools, and in
founding chapters of the Young Women's Christian Association. She also became a
successful author after her husband's death, writing a novel published by the
Congregational Sunday-School and Publishing Society, a biography of Margaret Junkin Preston,
and her own posthumously published memoirs.

Under Allan's leadership McDonogh Institute flourished. In 1885 he published a
biographical tribute to the philanthropy of the institute's founder, John McDonogh.
In Maryland Allan remained active in organizations as diverse as the Society of the
Army and Navy of the Confederate States, the Southern Historical Society, and the
Military Historical Society of Massachusetts. From 1873 until his death he was a trustee
of Washington and Lee University (as Washington College had become in 1871). He also
served on the board of the Lee Memorial Association and prepared the historical
sketch that the association used when raising money to build the Lee Mausoleum at Washington and Lee.
Allan died at his home at McDonogh School on September 17, 1889. Although his obituary
in the Baltimore Sun stated that Allan was to be buried in
Garrison Forest Cemetery, he was more likely interred in the churchyard at Saint Thomas's Episcopal Church.
His remains were then moved and reinterred in the Tagart Memorial Chapel at McDonogh
School on or about December 4, 1898.